Considerable effort is being made in sequencing the human genome. Information generated by this endeavor has already provided significant insights into the origin of a number of diseases, such as the discovery of specific gene variants associated with the incidence of Alzheimer's disease. Sequencing the human genome may alert us to the potential for specific gene products and measurements of messenger RNA can provide evidence of gene expression in specific tissues or cell types. However, if we are to understand normal and pathophysiological processes at the molecular level it will be essential to characterize expressed protein gene products. In contrast with studies of mRNA and genomic mapping and sequencing, studies of proteins allows for the examination of post-translational events, variations in protein synthesis and degradation, and the observation of exogenous gene products, such as those of viral origin. There were considerable hopes that high resolution two-dimensional protein electrophoresis would help facilitate this endeavor. In high-resolution two- dimensional protein electrophoresis, proteins are first separated by charge, and then by mass to produce a two dimensional array of proteins. However, current two-dimensional protein electrophoresis methodology has two major inadequacies that have hindered this endeavor. The first problem is the caused by the limits of sensitivity that are available for protein detection. One of the most sensitive methods currently available is silver staining. Silver staining can detect as little as 0.01 nanogram of protein. However, this level of detection is inadequate for the study of proteins in specific cells, such as those in the brain. The cellular heterogeneity of brain, in which glial cells generally surround and outnumber neurons 10 to 1, requires a technology that can detect proteins in single neuronal cells, if we are to decipher the underlying molecular events in the functioning of the central nervous system. While detection at 0.01 nanogram level may be adequate for some studies, it represents 20 million molecules of an average protein of molecular weight 30,000. As we have estimated that the average number of copies of specific proteins in a single cell range in the thousands and not in the millions the current protein detection technology is of little value. The second problem with current two-dimensional protein electrophoresis methodology involves our limited ability to characterize proteins that appear to be biologically interesting but present at the 0.01ng level. While the use of mass spectrometric analysis may help to alleviate this problem as the mass spectrometric techniques are refined, at this time analysis of trace proteins is still a problem. Given these problems, the laboratory is currently developing strategies and testing methods to alleviate these problems so that we can extend our knowledge of the brain in normal and diseased states.